Name of Molecule ______________________________________________________

How many chains are there?

Chain Name*

Protein, DNA, or RNA?

Number of Residues? **

Disulfides?

Alpha helices? ***

Beta strands? Parallel/antiparallel? ***

*Hint: click on the chain and look for the one-letter "name" in the
message window.
**Hint: use the Sequence display (click
PE Site Map,
then Sequences).
***Hint: in QuickViews, DISPLAY Cartoon, COLOR Structure.

Is water present?

Are bound ligands present (non-solvent "hetero" atoms)? If so, are they held
by covalent or noncovalent bonds? To what types of residues? (Hint: SELECT Ligand,
DISPLAY Contacts. Click on bonded atoms to identify their residues.)

In soluble proteins, hydrophobic residues are buried in the cores
of domains. Large hydrophobic patches on the surface may be sites of
protein-protein interaction. Where do you see concentrations of
hydrophobic residues? (Hint:
DISPLAY Spacefill, COLOR Polarity3.)

If there is protein bound to nucleic acid, which nucleotides
are recognized in a sequence-specific manner? Which are bound nonspecifically
to the backbone? (Hint: SELECT Protein, DISPLAY Contacts, click on bound
atoms to identify residues.)